PYTHONPATH extension?
Don't set PYTHONPATH, but rather add your script's path to sys.path. You can do that manually in Blender's Python Console, in a script you embed in a blend file via Blender's Text Editor, or in a small add-on that you place in a path that's already searched for by Blender.

Non-scripting approaches would be to set an alternative scripts folder in the user preferences, or to use symlinks to make Blender find your code.